Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review

Genomics and outbreak investigation: from sequence to consequence

(2016) Esther R Robinson et al.   Genome Medicine

Whole genome sequencing reveals genomic heterogeneity and antibiotic purification in Mycobacterium tuberculosis isolates

(2015) PA Black et al.   BMC GENOMICS

A Microbiological Revolution Meets an Ancient Disease: Improving the Management of Tuberculosis with Genomics

(2015) Marta Wlodarska et al.   CLINICAL MICROBIOLOGY REVIEWS

The application of genomics to tracing bacterial pathogen transmission

(2015) Nicholas J Croucher et al.   CURRENT OPINION IN MICROBIOLOGY

Clinical Application of Whole-Genome Sequencing To Inform Treatment for Multidrug-Resistant Tuberculosis Cases

(2015) Adam A. Witney et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Reemergence and Amplification of Tuberculosis in the Canadian Arctic

(2015) Robyn S. Lee et al.   JOURNAL OF INFECTIOUS DISEASES

Clinical value of whole-genome sequencing of Mycobacterium tuberculosis

(2015) Howard E Takiff et al.   LANCET INFECTIOUS DISEASES

Whole genome sequence analysis of multidrug-resistant Mycobacterium tuberculosis Beijing isolates from an outbreak in Thailand

(2015) Sanjib Mani Regmi et al.   MOLECULAR GENETICS AND GENOMICS

Whole Genome Sequencing Investigation of a Tuberculosis Outbreak in Port-au-Prince, Haiti Caused by a Strain with a “Low-Level” rpoB Mutation L511P – Insights into a Mechanism of Resistance Escalation

(2015) Oksana Ocheretina et al.   PLoS One

Diversity and disease pathogenesis in Mycobacterium tuberculosis

(2015) Digby F. Warner et al.   TRENDS IN MICROBIOLOGY

Within patient microevolution of Mycobacterium tuberculosis correlates with heterogeneous responses to treatment

(2015) Qingyun Liu et al.   Scientific Reports

Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area

(2015) JA Guerra-Assunção et al.   eLife

Enhanced tuberculosis outbreak investigation using whole genome sequencing and IGRA

(2014) P. W. Smit et al.   EUROPEAN RESPIRATORY JOURNAL

Whole genome sequencing reveals potential spread of Clostridium difficile between humans and farm animals in the Netherlands, 2002 to 2011

(2014) C Knetsch et al.   Eurosurveillance

The Distribution of Pairwise Genetic Distances: A Tool for Investigating Disease Transmission

(2014) Colin J. Worby et al.   GENETICS

Tracking a Tuberculosis Outbreak Over 21 Years: Strain-Specific Single-Nucleotide Polymorphism Typing Combined With Targeted Whole-Genome Sequencing

(2014) David Stucki et al.   JOURNAL OF INFECTIOUS DISEASES

Recurrence due to Relapse or Reinfection WithMycobacterium tuberculosis: A Whole-Genome Sequencing Approach in a Large, Population-Based Cohort With a High HIV Infection Prevalence and Active Follow-up

(2014) José Afonso Guerra-Assunção et al.   JOURNAL OF INFECTIOUS DISEASES

Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID): an extension of the STROBE statement

(2014) Nigel Field et al.   LANCET INFECTIOUS DISEASES

Bayesian Inference of Infectious Disease Transmission from Whole-Genome Sequence Data

(2014) Xavier Didelot et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution and transmission of drug-resistant tuberculosis in a Russian population

(2014) Nicola Casali et al.   NATURE GENETICS

Genomic insights into tuberculosis

(2014) James E. Galagan   NATURE REVIEWS GENETICS

Four-Month Moxifloxacin-Based Regimens for Drug-Sensitive Tuberculosis

(2014) Stephen H. Gillespie et al.   NEW ENGLAND JOURNAL OF MEDICINE

Whole Genome Sequencing of Mycobacterium tuberculosis Reveals Slow Growth and Low Mutation Rates during Latent Infections in Humans

(2014) Roberto Colangeli et al.   PLoS One

Marked Microevolution of a Unique Mycobacterium tuberculosis Strain in 17 Years of Ongoing Transmission in a High Risk Population

(2014) Carolina Mehaffy et al.   PLoS One

Supersize me: how whole-genome sequencing and big data are transforming epidemiology

(2014) Rowland R. Kao et al.   TRENDS IN MICROBIOLOGY

Whole-genome sequencing to detect recent transmission of Mycobacterium tuberculosis in settings with a high burden of tuberculosis

(2014) Tao Luo et al.   TUBERCULOSIS

Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

(2014) Thibaut Jombart et al.   PLoS Computational Biology

Assessment of Mycobacterium tuberculosis transmission in Oxfordshire, UK, 2007–12, with whole pathogen genome sequences: an observational study

(2014) Timothy M Walker et al.   Lancet Respiratory Medicine

Inferring patient to patient transmission of Mycobacterium tuberculosisfrom whole genome sequencing data

(2013) Josephine M Bryant et al.   BMC INFECTIOUS DISEASES

Rapid diagnostics of tuberculosis and drug resistance in the industrialized world: clinical and public health benefits and barriers to implementation

(2013) Francis Drobniewski et al.   BMC Medicine

A survey of tools for variant analysis of next-generation genome sequencing data

(2013) S. Pabinger et al.   BRIEFINGS IN BIOINFORMATICS

Contact investigations for outbreaks of Mycobacterium tuberculosis: advances through whole genome sequencing

(2013) T.M. Walker et al.   CLINICAL MICROBIOLOGY AND INFECTION

Selected insights from application of whole-genome sequencing for outbreak investigations

(2013) Vien Thi Minh Le et al.   Current Opinion in Critical Care

Relating Phylogenetic Trees to Transmission Trees of Infectious Disease Outbreaks

(2013) Rolf J. F. Ypma et al.   GENETICS

Multidrug-Resistant Tuberculosis in Panama Is Driven by Clonal Expansion of a Multidrug-Resistant Mycobacterium tuberculosis Strain Related to the KZN Extensively Drug-Resistant M. tuberculosis Strain from South Africa

(2013) F. Lanzas et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Whole Genome Sequencing Analysis of Intrapatient Microevolution in Mycobacterium tuberculosis: Potential Impact on the Inference of Tuberculosis Transmission

(2013) Laura Pérez-Lago et al.   JOURNAL OF INFECTIOUS DISEASES

Use of Whole Genome Sequencing to Determine the Microevolution of Mycobacterium tuberculosis during an Outbreak

(2013) Midori Kato-Maeda et al.   PLoS One

Whole Genome Sequencing Reveals Complex Evolution Patterns of Multidrug-Resistant Mycobacterium tuberculosis Beijing Strains in Patients

(2013) Matthias Merker et al.   PLoS One

Elucidating Emergence and Transmission of Multidrug-Resistant Tuberculosis in Treatment Experienced Patients by Whole Genome Sequencing

(2013) Taane G. Clark et al.   PLoS One

Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study

(2013) Andreas Roetzer et al.   PLOS MEDICINE

Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: a retrospective observational study

(2013) Josephine M Bryant et al.   Lancet Respiratory Medicine

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

Mixed-Strain Mycobacterium tuberculosis Infections and the Implications for Tuberculosis Treatment and Control

(2012) T. Cohen et al.   CLINICAL MICROBIOLOGY REVIEWS

Dynamic Population Changes in Mycobacterium tuberculosis During Acquisition and Fixation of Drug Resistance in Patients

(2012) Gang Sun et al.   JOURNAL OF INFECTIOUS DISEASES

Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study

(2012) Timothy M Walker et al.   LANCET INFECTIOUS DISEASES

Rapid Whole-Genome Sequencing for Investigation of a Neonatal MRSA Outbreak

(2012) Claudio U. Köser et al.   NEW ENGLAND JOURNAL OF MEDICINE

Mycobacterium tuberculosis – Heterogeneity revealed through whole genome sequencing

(2012) Chris Ford et al.   TUBERCULOSIS

Insights from Genomics into Bacterial Pathogen Populations

(2012) Daniel J. Wilson   PLoS Pathogens

Genotyping ofMycobacterium tuberculosis: application in epidemiologic studies

(2011) Midori Kato-Maeda et al.   Future Microbiology

The impact of next-generation sequencing on genomics

(2011) Jun Zhang et al.   Journal of Genetics and Genomics

Deep resequencing of serial sputum isolates of Mycobacterium tuberculosis during therapeutic failure due to poor compliance reveals stepwise mutation of key resistance genes on an otherwise stable genetic background

(2011) Nigel J. Saunders et al.   JOURNAL OF INFECTION

Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection

(2011) Christopher B Ford et al.   NATURE GENETICS

Whole-Genome Sequencing and Social-Network Analysis of a Tuberculosis Outbreak

(2011) Jennifer L. Gardy et al.   NEW ENGLAND JOURNAL OF MEDICINE

Sequential Bottlenecks Drive Viral Evolution in Early Acute Hepatitis C Virus Infection

(2011) Rowena A. Bull et al.   PLoS Pathogens

The non-clonality of drug resistance in Beijing-genotype isolates of Mycobacterium tuberculosis from the Western Cape of South Africa

(2010) Thomas R Ioerger et al.   BMC GENOMICS

Reconstructing disease outbreaks from genetic data: a graph approach

(2010) T Jombart et al.   HEREDITY

Microevolution of Mycobacterium tuberculosis in a Tuberculosis Patient

(2010) S. A. M. Al-Hajoj et al.   JOURNAL OF CLINICAL MICROBIOLOGY

High-Resolution Typing by Integration of Genome Sequencing Data in a Large Tuberculosis Cluster

(2010) A. C. Schurch et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Genomic Diversity among Drug Sensitive and Multidrug Resistant Isolates of Mycobacterium tuberculosis with Identical DNA Fingerprints

(2009) Stefan Niemann et al.   PLoS One

Genotyping of Genetically Monomorphic Bacteria: DNA Sequencing in Mycobacterium tuberculosis Highlights the Limitations of Current Methodologies

(2009) Iñaki Comas et al.   PLoS One